Gloria Li
Tue Jun 24 16:13:31 2014
| No.isoform.exons | No.isoform.genes | No.exons.with.junction.cov | No.genes.with.junction.cov | No.exons.with.junction.support | No.genes.with.junction.support | |
|---|---|---|---|---|---|---|
| lum084_myo084 | 8630 | 2381 | 3618 | 1228 | 3604 | 1217 |
| lum084_stem084 | 8948 | 2429 | 4226 | 1411 | 4217 | 1404 |
| myo084_stem084 | 8619 | 2427 | 3346 | 1247 | 3333 | 1238 |
| lum080_myo080 | 12871 | 2325 | 1687 | 509 | 1235 | 397 |
| lum080_stem080 | 8688 | 2345 | 1559 | 686 | 1232 | 559 |
| myo080_stem080 | 8448 | 2390 | 1105 | 548 | 791 | 427 |
| lum035_myo035 | 12911 | 2341 | 3536 | 817 | 2324 | 619 |
If a gene has only a few exons (\(\le\) 5 exons), and one exon is absent in one sample, i.e. isoform, the absence can bias the overall gene RPKM and this gene may be identified as a DE gene. Check if there are such cases.
For DE gene with small No. of exons:
* If it is in fact an isoform, not DE gene, only one / few exons in this gene should be differentially expressed.
* If it is a truly DE gene, all exons should be differentially expressed.
Proportion of DE exons for DE genes with \(\le\) 5 exons: (DE exons: fold change \(\ge\) 2)
* Proportion of DE exons < 1 for the few genes are due to exons not expressed in either samples.
* There is no evidence for isoforms genes identified as DE genes.
* Exon usage along the gene for all multi-transcript genes